I use joomla 1.5.22 + last JoomSEF + JSN Epic 3.5.0 template (demo: h__p://demo.joomlashine.com/joomla-templates/jsn_epic/)
If you turn ON JoomSEF, then SystemTools of template is not working (does not change the screen color and font size) - see cog in the upper right corner of the demo site.
If turned OFF JoomSEF, SystemTools of template works.
Where to find the problem?